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422ef0420f
Some tests fail on aarch64-darwin when SciPy is built with a newer compiler (such as clang 16). This is not yet fixed upstream, so disable them until they work again. See https://github.com/scipy/scipy/issues/18308
222 lines
6.1 KiB
Nix
222 lines
6.1 KiB
Nix
{ lib
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, stdenv
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, fetchFromGitHub
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, fetchpatch
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, fetchurl
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, writeText
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, python
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, pythonOlder
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, buildPythonPackage
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, cython
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, gfortran
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, meson-python
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, pkg-config
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, pythran
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, wheel
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, nose
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, pytestCheckHook
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, pytest-xdist
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, numpy
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, pybind11
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, pooch
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, libxcrypt
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, xsimd
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, blas
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, lapack
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}:
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let
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pname = "scipy";
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# DON'T UPDATE THESE ATTRIBUTES MANUALLY - USE:
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#
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# nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
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#
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# The update script uses sed regexes to replace them with the updated hashes.
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version = "1.11.2";
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srcHash = "sha256-7FE740/yKUXtujVX60fQB/xvCZFfV69FRihvSi6+UWo=";
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datasetsHashes = {
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ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
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ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
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face = "11i8x29h80y7hhyqhil1fg8mxag5f827g33lhnsf44qk116hp2wx";
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};
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datasets = lib.mapAttrs (
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d: hash: fetchurl {
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url = "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat";
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sha256 = hash;
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}
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) datasetsHashes;
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# Additional cross compilation related properties that scipy reads in scipy/meson.build
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crossFileScipy = writeText "cross-file-scipy.conf" ''
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[properties]
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numpy-include-dir = '${numpy}/${python.sitePackages}/numpy/core/include'
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pythran-include-dir = '${pythran}/${python.sitePackages}/pythran'
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host-python-path = '${python.interpreter}'
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host-python-version = '${python.pythonVersion}'
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'';
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in buildPythonPackage {
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inherit pname version;
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format = "pyproject";
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src = fetchFromGitHub {
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owner = "scipy";
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repo = pname;
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rev = "v${version}";
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hash = srcHash;
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fetchSubmodules = true;
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};
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patches = [
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# Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167
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(fetchpatch {
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url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch";
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hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s=";
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excludes = [
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"doc/source/dev/contributor/meson_advanced.rst"
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];
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})
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];
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# Relax deps a bit
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postPatch = ''
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substituteInPlace pyproject.toml \
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--replace 'numpy==' 'numpy>=' \
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--replace "pybind11>=2.10.4,<2.11.0" "pybind11>=2.10.4,<2.12.0" \
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--replace 'wheel<0.41.0' 'wheel'
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'';
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nativeBuildInputs = [
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cython
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gfortran
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meson-python
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pythran
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pkg-config
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wheel
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];
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buildInputs = [
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blas
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lapack
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pybind11
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pooch
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xsimd
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] ++ lib.optionals (pythonOlder "3.9") [
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libxcrypt
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];
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propagatedBuildInputs = [ numpy ];
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__darwinAllowLocalNetworking = true;
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nativeCheckInputs = [
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nose
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pytestCheckHook
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pytest-xdist
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];
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# The following tests are broken on aarch64-darwin with newer compilers and library versions.
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# See https://github.com/scipy/scipy/issues/18308
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disabledTests = lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [
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"test_a_b_neg_int_after_euler_hypergeometric_transformation"
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"test_dst4_definition_ortho"
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"test_load_mat4_le"
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"hyp2f1_test_case47"
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"hyp2f1_test_case3"
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"test_uint64_max"
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];
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doCheck = !(stdenv.isx86_64 && stdenv.isDarwin);
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preConfigure = ''
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# Helps parallelization a bit
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export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
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# We download manually the datasets and this variable tells the pooch
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# library where these files are cached. See also:
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# https://github.com/scipy/scipy/pull/18518#issuecomment-1562350648 And at:
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# https://github.com/scipy/scipy/pull/17965#issuecomment-1560759962
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export XDG_CACHE_HOME=$PWD; export HOME=$(mktemp -d); mkdir scipy-data
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'' + (lib.concatStringsSep "\n" (lib.mapAttrsToList (d: dpath:
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# Actually copy the datasets
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"cp ${dpath} scipy-data/${d}.dat"
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) datasets));
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mesonFlags = [
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"-Dblas=${blas.pname}"
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"-Dlapack=${lapack.pname}"
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# We always run what's necessary for cross compilation, which is passing to
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# meson the proper cross compilation related arguments. See also:
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# https://docs.scipy.org/doc/scipy/building/cross_compilation.html
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"--cross-file=${crossFileScipy}"
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];
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# disable stackprotector on aarch64-darwin for now
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#
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# build error:
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#
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# /private/tmp/nix-build-python3.9-scipy-1.6.3.drv-0/ccDEsw5U.s:109:15: error: index must be an integer in range [-256, 255].
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#
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# ldr x0, [x0, ___stack_chk_guard];momd
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#
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hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ];
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checkPhase = ''
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runHook preCheck
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# Adapted from pytestCheckHook because scipy uses a custom check phase.
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# It needs to pass `$args` as a Python list to `scipy.test` rather than as
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# arguments to pytest on the command-line.
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args=""
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if [ -n "$disabledTests" ]; then
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disabledTestsString=$(_pytestComputeDisabledTestsString "''${disabledTests[@]}")
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args+="'-k','$disabledTestsString'"
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fi
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if [ -n "''${disabledTestPaths-}" ]; then
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eval "disabledTestPaths=($disabledTestPaths)"
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fi
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for path in ''${disabledTestPaths[@]}; do
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if [ ! -e "$path" ]; then
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echo "Disabled tests path \"$path\" does not exist. Aborting"
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exit 1
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fi
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args+="''${args:+,}'--ignore=\"$path\"'"
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done
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args+="''${args:+,}$(printf \'%s\', "''${pytestFlagsArray[@]}")"
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args=''${args%,}
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pushd "$out"
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export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 ))
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${python.interpreter} -c "import scipy, sys; sys.exit(scipy.test(
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'fast',
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verbose=10,
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extra_argv=[$args],
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parallel=$NIX_BUILD_CORES
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) != True)"
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popd
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runHook postCheck
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'';
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requiredSystemFeatures = [ "big-parallel" ]; # the tests need lots of CPU time
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passthru = {
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inherit blas;
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updateScript = [
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./update.sh
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# Pass it this file name as argument
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(builtins.unsafeGetAttrPos "pname" python.pkgs.scipy).file
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]
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# Pass it the names of the datasets to update their hashes
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++ (builtins.attrNames datasetsHashes)
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;
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};
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SCIPY_USE_G77_ABI_WRAPPER = 1;
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meta = with lib; {
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description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering";
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homepage = "https://www.scipy.org/";
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license = licenses.bsd3;
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maintainers = with maintainers; [ fridh doronbehar ];
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};
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}
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